multifreqpoly {ENmix} | R Documentation

## Multiple frequency polygon plot

### Description

Produce Frequency polygon plot for each column of a numeric data matrix. Similar to multidensity function, the plot can be used to inspect data distribution but with much faster speed.

### Usage

    multifreqpoly(mat, nbreaks=100, col=1:ncol(mat), xlab="",
                  ylab="Frequency",legend = list(x = "top", fill=col,
                  legend = if(is.null(colnames(mat))) paste(1:ncol(mat))
                  else colnames(mat)),append=FALSE,...)

### Arguments

`mat` | A numeric matrix
`nbreaks` | The number of bins for frequency counting
`col` | Line plot color code, the length should be equal to the number of columns in mat
`xlab` | x-axis lable
`ylab` | y-axis lable
`legend` | A list of arguments that get passed to the function "legend"
`append` | TRUE or FALSE, whether to create a new figure or append to the current figure.
`...` | Further arguments that get passed to the function "plot"

### Value

Frequency polygon plots.

### Author(s)

Zongli Xu

### References

Zongli Xu, Liang Niu, Leping Li and Jack A. Taylor, ENmix: a novel background correction method for Illumina HumanMethylation450 BeadChip. Nucleic Acids Research 2015.

### Examples

    x=matrix(rnorm(10000),nrow=2000,ncol=5)
    multifreqpoly(x,nbreaks=15,legend=list(x="topright",fill=1:ncol(x),legend=paste("V",1:5,sep="")))

    if (require(minfiData)) {
    path <- file.path(find.package("minfiData"),"extdata")
    rgSet <- readidat(path = path,recursive = TRUE)
    mraw <- getmeth(rgSet)
    beta<-getB(mraw)
    jpeg("dist_raw.jpg")
    multifreqpoly(beta,col=1:ncol(beta))
    dev.off()
    }

[Package ENmix version 1.30.03 Index]